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Accelerating de bruijn graph-based genome assembly for high-throughput short read data

 
: Zhao, K.; Liu, W.; Voss, G.; Mueller-Wittig, W.

:

IEEE Computer Society:
19th IEEE International Conference on Parallel and Distributed Systems, ICPADS 2013 : Seoul, South Korea, 15 - 18 December 2013
Piscataway, NJ: IEEE, 2013
ISBN: 978-1-4799-2082-2
ISBN: 978-1-4799-2081-5
S.426-427
International Conference on Parallel and Distributed Systems (ICPADS) <19, 2013, Seoul>
Englisch
Konferenzbeitrag
Fraunhofer IDM@NTU ()

Abstract
Emerging next-generation sequencing technologies have opened up exciting new opportunities for genome sequencing by generating read data with a massive throughput. However, the generated reads are significantly shorter compared to the traditional Sanger shotgun sequencing method. This poses challenges for de novo assembly algorithms in terms of both accuracy and efficiency. And due to the continuing explosive growth of short read databases, there is a high demand to accelerate the often repeated long-runtime assembly task. In this paper, we present a scalable parallel algorithm to accelerate the de Bruijn graph-based genome assembly for high-throughput short read data.

: http://publica.fraunhofer.de/dokumente/N-300875.html